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### 5.1 A2Xml

A2Xml is dedicated to convert plaint text files into XML files compliant with the analysis programs of MetaQTL.

#### 5.1.1 Command Line Options

Option | Usage | Type | Explanation
--- | --- | --- | ---
`-i,--ifile` | required | string | The file to convert in XML.
`-x,--xmlfile` | required | string | The output XML file.
`-t,--type` | required | string | The type of the input file.
`-f,--format` | optional | string | The format of the input file.

Presently, the command `--type` have two possible values:

- `map` : the input file is a marker and/or QTL map.
- `onto` : the input file is an ontology.

         %java org.metatqtl.main.A2Xml \
         >     -i map.txt -x map.xml -t map -f chart

The command `-f,--format` allows user to convert into XML different input file formats. This option works only when `-t,--type` is set to `map`. In this case 3 different input file formats can be used:

- `tab` : the map is in tabulated format as for the GLMdb tables See GLMdb.
- `mch` : the map is formatted like a MapChart (Voorrips 2002) input file.
- `mmk` : the map is formatted like a MapMaker (Lander 1987) output.

For example, suppose we have a map file `map.txt` in tabulated format as follows,

         group   marker  position
         1       umc11   0.0
         1       gsy27   18.0
         1       umc67   54.0
         1       umc58   75.0
         1       umc83a  115.0
         1       umc66b  140.0
         1       gsy56   153.0
         1       umc161  168.0
         1       umc84   189.0
         1       bnl6.32 198.0

Then we can convert it into a XML file using the command

         %java org.metatqtl.main.A2Xml \
         >     -i map.txt -x map.xml -t map -f tab

This creates a file named `map.xml` which looks like this

         <?xml version="1.0" encoding="UTF-8"?>
         <genome-map name="">
          <linkage-group name="1">
           <locus name="umc83a" type="M" position="115.0"/>
           <locus name="bnl6.32" type="M" position="198.0"/>
           <locus name="gsy27" type="M" position="18.0"/>
           <locus name="umc58" type="M" position="75.0"/>
           <locus name="umc161" type="M" position="168.0"/>
           <locus name="umc66b" type="M" position="140.0"/>
           <locus name="umc11" type="M" position="0.0"/>
           <locus name="gsy56" type="M" position="153.0"/>
           <locus name="umc67" type="M" position="54.0"/>
           <locus name="umc84" type="M" position="189.0"/>
          </linkage-group>
         </genome-map>

The XML file will be the same if instead using a tabulated format we have used a MapChart format as input

         group 1
         umc11 0
         gsy27 18
         umc67 54
         umc58 75
         umc83a 115
         umc66b 140
         gsy56 153
         umc161 168
         umc84 189
         bnl6.32 198

and the command

         %java org.metatqtl.main.A2Xml \
         >     -i map.txt -x map.xml -t map -f chart

or if we have used a MapMaker like format

         *1
         >map
         ===========================================================================
         Map:
           Markers         Distance
            1  umc11         18 cM
            2  gsy27         36 cM
            3  umc67         21 cM
            4  umc58         40 cM
            5  umc83a        25 cM
            6  umc66b        13 cM
            7  gsy56         15 cM
            8  umc161        21 cM
            9  umc84          9 cM
            10  bnl6.32     ----------
                         198 cM 10 markers   log-likelihood=
         ===========================================================================

and the command

         %java org.metatqtl.main.A2Xml \
         >     -i map.txt -x map.xml -t map -f mm